A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease
In recent years, next-generation sequencing (NGS) was employed to decipher the structure and composition of the microbiota of the airways in cystic fibrosis (CF) patients. However, little is still known about the overall gene functions harbored by the resident microbial populations and which specifi...
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2017-07-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/18/8/1654 |
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doaj-fa4aa103346d40529f11f1f0eeebb7de2020-11-25T00:16:18ZengMDPI AGInternational Journal of Molecular Sciences1422-00672017-07-01188165410.3390/ijms18081654ijms18081654A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung DiseaseGiovanni Bacci0Alessio Mengoni1Ersilia Fiscarelli2Nicola Segata3Giovanni Taccetti4Daniela Dolce5Patrizia Paganin6Patrizia Morelli7Vanessa Tuccio8Alessandra De Alessandri9Vincenzina Lucidi10Annamaria Bevivino11Department of Biology, University of Florence, Florence 50019, ItalyDepartment of Biology, University of Florence, Florence 50019, ItalyCystic Fibrosis Microbiology and Cystic Fibrosis Center, “Bambino Gesù” Children’s Hospital and Research Institute, Rome 00165, ItalyCentre for Integrative Biology, University of Trento, Trento 38123, ItalyDepartment of Pediatric Medicine, Cystic Fibrosis Center, Anna Meyer Children’s University Hospital, Florence 50139, ItalyDepartment of Pediatric Medicine, Cystic Fibrosis Center, Anna Meyer Children’s University Hospital, Florence 50139, ItalyTerritorial and Production Systems Sustainability Department, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, Rome 00123, ItalyCystic Fibrosis Center, IRCCS G. Gaslini Institute, Genoa 16146, ItalyCystic Fibrosis Microbiology and Cystic Fibrosis Center, “Bambino Gesù” Children’s Hospital and Research Institute, Rome 00165, ItalyCystic Fibrosis Center, IRCCS G. Gaslini Institute, Genoa 16146, ItalyCystic Fibrosis Microbiology and Cystic Fibrosis Center, “Bambino Gesù” Children’s Hospital and Research Institute, Rome 00165, ItalyTerritorial and Production Systems Sustainability Department, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, Rome 00123, ItalyIn recent years, next-generation sequencing (NGS) was employed to decipher the structure and composition of the microbiota of the airways in cystic fibrosis (CF) patients. However, little is still known about the overall gene functions harbored by the resident microbial populations and which specific genes are associated with various stages of CF lung disease. In the present study, we aimed to identify the microbial gene repertoire of CF microbiota in twelve patients with severe and normal/mild lung disease by performing sputum shotgun metagenome sequencing. The abundance of metabolic pathways encoded by microbes inhabiting CF airways was reconstructed from the metagenome. We identified a set of metabolic pathways differently distributed in patients with different pulmonary function; namely, pathways related to bacterial chemotaxis and flagellar assembly, as well as genes encoding efflux-mediated antibiotic resistance mechanisms and virulence-related genes. The results indicated that the microbiome of CF patients with low pulmonary function is enriched in virulence-related genes and in genes encoding efflux-mediated antibiotic resistance mechanisms. Overall, the microbiome of severely affected adults with CF seems to encode different mechanisms for the facilitation of microbial colonization and persistence in the lung, consistent with the characteristics of multidrug-resistant microbial communities that are commonly observed in patients with severe lung disease.https://www.mdpi.com/1422-0067/18/8/1654cystic fibrosislung diseaselung microbiomeshotgun metagenomicsbioinformaticsmetabolic pathwaysvirulence genes |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Giovanni Bacci Alessio Mengoni Ersilia Fiscarelli Nicola Segata Giovanni Taccetti Daniela Dolce Patrizia Paganin Patrizia Morelli Vanessa Tuccio Alessandra De Alessandri Vincenzina Lucidi Annamaria Bevivino |
| spellingShingle |
Giovanni Bacci Alessio Mengoni Ersilia Fiscarelli Nicola Segata Giovanni Taccetti Daniela Dolce Patrizia Paganin Patrizia Morelli Vanessa Tuccio Alessandra De Alessandri Vincenzina Lucidi Annamaria Bevivino A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease International Journal of Molecular Sciences cystic fibrosis lung disease lung microbiome shotgun metagenomics bioinformatics metabolic pathways virulence genes |
| author_facet |
Giovanni Bacci Alessio Mengoni Ersilia Fiscarelli Nicola Segata Giovanni Taccetti Daniela Dolce Patrizia Paganin Patrizia Morelli Vanessa Tuccio Alessandra De Alessandri Vincenzina Lucidi Annamaria Bevivino |
| author_sort |
Giovanni Bacci |
| title |
A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease |
| title_short |
A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease |
| title_full |
A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease |
| title_fullStr |
A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease |
| title_full_unstemmed |
A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease |
| title_sort |
different microbiome gene repertoire in the airways of cystic fibrosis patients with severe lung disease |
| publisher |
MDPI AG |
| series |
International Journal of Molecular Sciences |
| issn |
1422-0067 |
| publishDate |
2017-07-01 |
| description |
In recent years, next-generation sequencing (NGS) was employed to decipher the structure and composition of the microbiota of the airways in cystic fibrosis (CF) patients. However, little is still known about the overall gene functions harbored by the resident microbial populations and which specific genes are associated with various stages of CF lung disease. In the present study, we aimed to identify the microbial gene repertoire of CF microbiota in twelve patients with severe and normal/mild lung disease by performing sputum shotgun metagenome sequencing. The abundance of metabolic pathways encoded by microbes inhabiting CF airways was reconstructed from the metagenome. We identified a set of metabolic pathways differently distributed in patients with different pulmonary function; namely, pathways related to bacterial chemotaxis and flagellar assembly, as well as genes encoding efflux-mediated antibiotic resistance mechanisms and virulence-related genes. The results indicated that the microbiome of CF patients with low pulmonary function is enriched in virulence-related genes and in genes encoding efflux-mediated antibiotic resistance mechanisms. Overall, the microbiome of severely affected adults with CF seems to encode different mechanisms for the facilitation of microbial colonization and persistence in the lung, consistent with the characteristics of multidrug-resistant microbial communities that are commonly observed in patients with severe lung disease. |
| topic |
cystic fibrosis lung disease lung microbiome shotgun metagenomics bioinformatics metabolic pathways virulence genes |
| url |
https://www.mdpi.com/1422-0067/18/8/1654 |
| work_keys_str_mv |
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